diff --git a/models/viralspread/netlogo/ViralSpread.nlogo b/models/viralspread/netlogo/ViralSpread.nlogo index 731692a..938496a 100644 --- a/models/viralspread/netlogo/ViralSpread.nlogo +++ b/models/viralspread/netlogo/ViralSpread.nlogo @@ -1,29 +1,36 @@ ;; ----- DECLARATIONS ----- +;; use arrays +extensions [array] + ;; Create "breed" of 'turtle' called cell breed [cells cell] ;; eventually separate mesophyll? breed [vasculars vascular] ;; phloem vascular bundles ;; Create "breed" of 'link' called phloem -directed-link-breed [phloems phloem] +undirected-link-breed [phloems phloem] ;; Note: I know there shouldn't be an s, but it wanted a different plural :( undirected-link-breed [plasmodesmata plasmodesma] +directed-link-breed [tests test] + ;; Declare global variables globals [ num-infected ;; keep track of number infected num-viruses ;; keep track of the viral particles - mod-num-viruses ;; keep track of the modified viral particles - lysed-cells ;; keep track of apoptotic cells + mod-num-viruses ;; keep track of the modified viral particles + lysed-cells ;; keep track of apoptotic cells + infect-per-leaf ;; array of infection counts + mod-infect-per-leaf ;; array of mod-infection counts ] ;; Declare the cell-specific (turtle breed) variables -cells-own +turtles-own [ infected? ;; if true, the cell is infectious resistant? ;; if true, cell can't be infected num-plasmodesmata ;; number of connections with other cells - copy-number ;; track the number of genomes in the nucleus + copy-number ;; track the number of genomes in the nucleus ;;; not used currently pregenomes ;; track the number of pregenomes in the cell protein-six ;; track functional P6 viral-count ;; keeps track of the virions produced by the cell @@ -31,6 +38,7 @@ cells-own mod-pregenomes ;; as above with delta-P6 mod-viral-count ;; as above with delta-P6 sar-level ;; amount of "salicylic acid" present in the cell + leaf ;; leaf number ] @@ -39,14 +47,16 @@ cells-own ;; Setup procedures to setup - clear-all ;; remove anything from previous runs - setup-stem ;; make a stem structure to connect the leaves - setup-cells ;; set up the cells - setup-leaf ;; set up the connections between cells - ask n-of initial-infection-sites cells ;; infect this number of cells + clear-all ;; remove anything from previous runs + random-seed 1 ;; consistent seed for reproducibility -- useful in debugging & screenshots + setup-cells ;; set up the cells and group them in leaves + setup-leaf ;; set up the connections between cells and connect the stems + set infect-per-leaf array:from-list n-values num-leaves [0] ;; initialize as 1xn array of 0's + set mod-infect-per-leaf array:from-list n-values num-leaves [0] ;; initialize as 1xn array of 0's + ask n-of initial-infection-sites cells with [leaf = 0] ;; infect this number of cells [ become-infected - set copy-number founder-population-viruses ;; start with x genomes per infected cell + set viral-count founder-population-viruses ;; start with x genomes per infected cell ] ask links [ set color white ] ;; make the symplastic connections white ask phloems @@ -55,96 +65,110 @@ to setup set thickness 0.3 ] reset-ticks ;; reset timer from previous run + if file-exists? "netlogo_out.csv" [file-delete "netlogo_out.csv"] ;; clean slate for output end -to setup-stem + +to setup-cells + set-default-shape cells "circle" ;; uses circle shape for displayed cells + let cells-per-leaf floor (num-cells / num-leaves) + let extra-cells remainder num-cells num-leaves + let angular-spacing 10 ;; degrees between leaves + if angular-spacing * num-leaves > 360 ;; throw an error if the leaves don't fit + [ error "Not enough space for leaves"] + let leaf-angle (360 - angular-spacing * num-leaves) / num-leaves ;; angular width per leaf + let rmin 0.1 * max-pxcor ;; minimum distrance from the origin + let rmax min list max-pxcor max-pycor ;; max distance -- + + foreach n-values extra-cells [?] ;; ? here is just identity, making n-values 0:n-1 + [create-cells cells-per-leaf + 1 ;; + [ + set size 0.5 ;; netlogo is a freak, so '?' == loop iteration - 1 + let theta (? * (leaf-angle + angular-spacing)) + random-float leaf-angle + let r random-radius rmin rmax + let x r * cos(theta) + let y r * sin(theta) + setxy x y + set leaf ? ;; leaf number = loop iteration, starting from 0. + become-susceptible + ] + ] + ;; now do it again for leaves without extra cells + foreach n-values (num-leaves - extra-cells) [? + extra-cells] ;; ? here is just identity, making n-values 0:n-1 + [create-cells cells-per-leaf ;; + [ + set size 0.5 ;; netlogo is a freak, so '?' == loop iteration - 1 + let theta (? * (leaf-angle + angular-spacing)) + random-float leaf-angle + let r random-radius rmin rmax + let x r * cos(theta) + let y r * sin(theta) + setxy x y + set leaf ? ;; Leaf number = iteration + become-susceptible + ] + ] + ;; ---- also set up the stems here, since we use the same local variables + set-default-shape vasculars "plant" ;; uses stem-looking shape for vasculature ;; Create and position vascular cells - create-vasculars 1 [ setxy 0 -16 ] - create-vasculars 1 - [ - setxy 0 -6 - create-phloem-from vascular 0 ;; directed stem connection - ] - create-vasculars 1 - [ - setxy 0 6 - create-phloem-from vascular 1 ;; directed stem connection - ] - create-vasculars 1 - [ - setxy 0 16 - create-phloem-from vascular 2 ;; directed stem connection + create-vasculars num-leaves + 1 ;; one central vascular, plus one per leaf + ;; vasculature numbeing starts at num-cells -- each turtle has separate number + ask vascular num-cells + [become-susceptible] + foreach n-values num-leaves [?] + [ ask vascular (? + 1 + num-cells) + [ + let r (rmin + rmax) / 2 + let theta (? * (leaf-angle + angular-spacing)) + leaf-angle / 2 + setxy (r * cos(theta)) (r * sin(theta)) + create-phloem-with vascular num-cells ;; connect to central stem + ;; Connect to a cell in your own leaf + let choice ( one-of (cells with [leaf = ?]) ) + if choice != nobody [ create-phloem-with choice ] + become-susceptible + ] ] ask vasculars ;; make the vasculature stand out from the leaf cells [ set color green set size 2.5 - ] + ] end -to setup-cells - set-default-shape cells "circle" ;; uses circle shape for displayed cells - create-cells num-cells - [ - let xguess random-pxcor - while [abs xguess < 0.1 * max-pxcor or abs xguess > 0.95 * max-pxcor] - [set xguess random-pxcor] - - let yguess random-pycor - while [abs yguess < 0.1 * max-pycor or abs yguess > 0.95 * max-pycor] - [set yguess random-pycor] - - setxy xguess yguess ;; no nodes too close to edges - become-susceptible - ask cells [ set size 0.5 ] ;; makes the circles smaller for larger scale - ] +;; --- helper function to pick a radius that ensures unifom distribution --- +to-report random-radius [rmin rmax] + ;; picks a radius at random such that points will be uniform in a circle + ;; pdf is r/const ; use inverse transform method + let u random-float 1 + let r sqrt(u * (rmax ^ 2 - rmin ^ 2) + rmin ^ 2 ) + report r end + + to setup-leaf ask cells [ ;; using random-possion to give a more realistic distribution of links per cell + let my-leaf leaf while [ count my-links < random-poisson avg-num-plasmodesmata ] [ - let choice (min-one-of (other cells with [not link-neighbor? myself]) + let choice (min-one-of (other cells with [(not link-neighbor? myself) and leaf = my-leaf]) [distance myself]) if choice != nobody [ create-plasmodesma-with choice ] ] ] ;; to make the network look nicer - repeat 10 [ layout-spring turtles links 0.3 (world-width / (sqrt num-cells)) 1 ] - ;; connect leaves to the vasculature - ask vascular 0 - [ - let choice ( one-of (cells with [pxcor < 0 and pycor < 0]) ) - if choice != nobody [ create-phloem-from choice ] - ] - ask vascular 1 - [ - let choice ( one-of (cells with [pxcor > 0 and pycor < 0]) ) - if choice != nobody [ create-phloem-from choice ] - ] - ask vascular 2 - [ - let choice ( one-of (cells with [pxcor < 0 and pycor > 0]) ) - if choice != nobody [ create-phloem-from choice ] - ] - ask vascular 3 - [ - let choice ( one-of (cells with [pxcor > 0 and pycor > 0]) ) - if choice != nobody [ create-phloem-from choice ] - ] +repeat 10 [ layout-spring turtles links 0.3 (world-width / (sqrt num-cells)) 1 ] end - ;; ----- MAIN ----- ;; This is the main process - what is activated when the user clicks "go" to go - ;; if the user specified a duration, stop after that + ;; if the user specified a duration, stop after that. if specified-duration [ if ticks > num-ticks [ stop ] @@ -160,17 +184,33 @@ to go set i i + 1 tick ] - stop ;; stop model completely + stop + ;; stop model completely ] - - ;; otherwise, continue to spread the virus + ;; otherwise, continue to spread the virus spread-virus spread-sar do-apoptosis-checks + record-data tick end - +;; ----- DATA OUTPUT ----- + +to record-data + file-open "netlogo_out.csv" + let leaf-infect-list array:to-list infect-per-leaf + foreach leaf-infect-list ;; iterate through this list + [ file-write ? ;; type number then comma + file-type ","] + file-type " ," ;; next set of columns: mod infections + let mod-leaf-infect-list array:to-list mod-infect-per-leaf + foreach mod-leaf-infect-list ;; iterate through this list + [ file-write ? ;; type number then comma + file-type ","] + file-type "\n" ;; newline + file-close ;; apparently bad things happen if you don't +end ;; ----- CELL PROCEDURES ----- @@ -185,6 +225,7 @@ to become-infected ;set viral-count 0 ; new-viruses set copy-number copy-number + 1 set num-viruses num-viruses + 1 + array:set infect-per-leaf leaf (array:item infect-per-leaf leaf + 1) ;; increment counter end to mod-become-infected @@ -193,6 +234,7 @@ to mod-become-infected set color red set mod-copy-number copy-number + 1 set mod-num-viruses mod-num-viruses + 1 + array:set mod-infect-per-leaf leaf (array:item mod-infect-per-leaf leaf + 1) ;; increment counter end to become-susceptible @@ -211,12 +253,21 @@ end ;; ---- SAR Molecule Spread & Apoptosis ---- -;; Increase levels of signalling molecule based on neighbours' levels -;; Assuming the infected cells are unable to produce sar signal molecules, but +;; Signalling molecules are produced (one per tick) by +;; - cells with infected neighbours +;; - resistant cells +;; Signalling molecules are spread by +;; - resistant cells -- pass on 20% their SAR each tick +;; - susceptible cells -- only pass on 10% +;; - Stems also spread SAR, but don't produce any. +;; - Infected cells do not produce or pass on SAR, but they can lyse. +;; NOTE -- don't have an integer # of molecules, since they get split. to spread-sar ;; initial generation of sar based on neighbouring cells being infected ask cells [ + if (any? link-neighbors with [infected?]) + [ set sar-level sar-level + 1 ] let neighboured false ;; remember if a neighbour is infected ask link-neighbors [ @@ -224,28 +275,35 @@ to spread-sar ] ;; if a neighbour is infected, increase this cell's sar signalling molecule if (neighboured) [ set sar-level sar-level + 1 ] + if (resistant?) [set sar-level sar-level + 1 ] ] ;; assume the resistant cells are better able to spread the sar molecule - ask cells with [resistant?] + ask turtles with [resistant?] [ - let shared-sar sar-level / 2 ;; saying half the sar-level will be spread + let shared-sar sar-level / 5 ;; saying half the sar-level will be spread + let num-neighbors (count link-neighbors) ask link-neighbors [ - set sar-level sar-level + shared-sar - if sar-level >= resistance-threshold [ set resistant? true ] + set sar-level sar-level + shared-sar / num-neighbors + if (sar-level >= resistance-threshold) and (not infected?) + [ set resistant? true + set color blue ] ] - set sar-level sar-level + shared-sar / 2 ;; not much kept in the cell + set sar-level sar-level - shared-sar ;; take away what we spread ] ;; assume the susceptible cells can produce an okay amount of sar molecule - ask cells with [not infected? and not resistant?] + ask turtles with [not infected? and not resistant?] [ - let shared-sar sar-level / 5 ;; fifth of the molecules will be shared + let shared-sar sar-level / 10 ;; fifth of the molecules will be shared + let num-neighbors (count link-neighbors) ask link-neighbors [ - set sar-level sar-level + shared-sar - if sar-level >= resistance-threshold [ set resistant? true ] + set sar-level sar-level + shared-sar / num-neighbors + if (sar-level >= resistance-threshold) and (not infected?) + [ set resistant? true + set color blue ] ] - set sar-level sar-level + shared-sar / 2 + set sar-level sar-level - shared-sar ;; take away what we spread ] end @@ -269,9 +327,9 @@ end ;; Procedure governing spread to neighbouring cells to spread-virus - ask cells with [infected?] + ask turtles with [infected?] [ - if (viral-count + mod-viral-count > 500) + if (viral-count + mod-viral-count > -1) [ ask link-neighbors with [not resistant? and not infected?] [ @@ -382,8 +440,8 @@ SLIDER num-cells num-cells 1 -1000 -275 +300 +216 1 1 NIL @@ -398,7 +456,7 @@ avg-num-plasmodesmata avg-num-plasmodesmata 1 10 -6 +7 1 1 NIL @@ -448,7 +506,7 @@ viral-spread-chance viral-spread-chance 1 20 -9 +6.5 0.5 1 NIL @@ -463,7 +521,7 @@ num-ticks num-ticks 0 500 -167 +252 1 1 NIL @@ -476,7 +534,7 @@ SWITCH 223 specified-duration specified-duration -1 +0 1 -1000 @@ -505,11 +563,11 @@ SLIDER 174 founder-population-viruses founder-population-viruses -1 -30 +400 +600 +440 10 1 -1 NIL HORIZONTAL @@ -522,7 +580,7 @@ lysis-threshold lysis-threshold 1 10000 -10000 +2294 1 1 NIL @@ -555,7 +613,22 @@ resistance-threshold resistance-threshold 1 100 -89 +14 +1 +1 +NIL +HORIZONTAL + +SLIDER +24 +327 +196 +360 +num-leaves +num-leaves +1 +10 +7 1 1 NIL diff --git a/models/viralspread/netlogo/ViralSpread_goodlooking.nlogo b/models/viralspread/netlogo/ViralSpread_goodlooking.nlogo new file mode 100644 index 0000000..59960e8 --- /dev/null +++ b/models/viralspread/netlogo/ViralSpread_goodlooking.nlogo @@ -0,0 +1,1025 @@ +;; ----- DECLARATIONS ----- +;; use arrays +extensions [array] + +;; Create "breed" of 'turtle' called cell +breed [cells cell] ;; eventually separate mesophyll? +breed [vasculars vascular] ;; phloem vascular bundles + +;; Create "breed" of 'link' called phloem +undirected-link-breed [phloems phloem] +;; Note: I know there shouldn't be an s, but it wanted a different plural :( +undirected-link-breed [plasmodesmata plasmodesma] + +directed-link-breed [tests test] + +;; Declare global variables +globals +[ + num-infected ;; keep track of number infected + num-viruses ;; keep track of the viral particles + mod-num-viruses ;; keep track of the modified viral particles + lysed-cells ;; keep track of apoptotic cells + infect-per-leaf ;; array of infection counts + mod-infect-per-leaf ;; array of mod-infection counts +] + +;; Declare the cell-specific (turtle breed) variables +turtles-own +[ + infected? ;; if true, the cell is infectious + resistant? ;; if true, cell can't be infected + num-plasmodesmata ;; number of connections with other cells + copy-number ;; track the number of genomes in the nucleus ;;; not used currently + pregenomes ;; track the number of pregenomes in the cell + protein-six ;; track functional P6 + viral-count ;; keeps track of the virions produced by the cell + mod-copy-number ;; as above with delta-P6 + mod-pregenomes ;; as above with delta-P6 + mod-viral-count ;; as above with delta-P6 + sar-level ;; amount of "salicylic acid" present in the cell + leaf ;; leaf number +] + + + + + +;; Setup procedures +to setup + clear-all ;; remove anything from previous runs + random-seed 1 ;; consistent seed for reproducibility -- useful in debugging & screenshots + setup-cells ;; set up the cells and group them in leaves + setup-leaf ;; set up the connections between cells and connect the stems + set infect-per-leaf array:from-list n-values num-leaves [0] ;; initialize as 1xn array of 0's + set mod-infect-per-leaf array:from-list n-values num-leaves [0] ;; initialize as 1xn array of 0's + ask n-of initial-infection-sites cells with [leaf = 0] ;; infect this number of cells + [ + become-infected + set viral-count founder-population-viruses ;; start with x genomes per infected cell + ] + ask links [ set color white ] ;; make the symplastic connections white + ask phloems + [ + set color green ;; make the vascular bundles green and thicker + set thickness 0.3 + ] + reset-ticks ;; reset timer from previous run + if file-exists? "netlogo_out.csv" [file-delete "netlogo_out.csv"] ;; clean slate for output +end + + +to setup-cells + set-default-shape cells "circle" ;; uses circle shape for displayed cells + let cells-per-leaf floor (num-cells / num-leaves) + let extra-cells remainder num-cells num-leaves + let angular-spacing 10 ;; degrees between leaves + if angular-spacing * num-leaves > 360 ;; throw an error if the leaves don't fit + [ error "Not enough space for leaves"] + let leaf-angle (360 - angular-spacing * num-leaves) / num-leaves ;; angular width per leaf + let rmin 0.1 * max-pxcor ;; minimum distrance from the origin + let rmax min list max-pxcor max-pycor ;; max distance -- + + foreach n-values extra-cells [?] ;; ? here is just identity, making n-values 0:n-1 + [create-cells cells-per-leaf + 1 ;; + [ + set size 0.5 ;; netlogo is a freak, so '?' == loop iteration - 1 + let theta (? * (leaf-angle + angular-spacing)) + random-float leaf-angle + let r random-radius rmin rmax + let x r * cos(theta) + let y r * sin(theta) + setxy x y + set leaf ? ;; leaf number = loop iteration, starting from 0. + become-susceptible + ] + ] + ;; now do it again for leaves without extra cells + foreach n-values (num-leaves - extra-cells) [? + extra-cells] ;; ? here is just identity, making n-values 0:n-1 + [create-cells cells-per-leaf ;; + [ + set size 0.5 ;; netlogo is a freak, so '?' == loop iteration - 1 + let theta (? * (leaf-angle + angular-spacing)) + random-float leaf-angle + let r random-radius rmin rmax + let x r * cos(theta) + let y r * sin(theta) + setxy x y + set leaf ? ;; Leaf number = iteration + become-susceptible + ] + ] + ;; ---- also set up the stems here, since we use the same local variables + + set-default-shape vasculars "leaf" ;; uses stem-looking shape for vasculature + ;; Create and position vascular cells + create-vasculars num-leaves + 1 ;; one central vascular, plus one per leaf + ;; vasculature numbeing starts at num-cells -- each turtle has separate number + ask vascular num-cells + [become-susceptible + set shape "plant"] + foreach n-values num-leaves [?] + [ ask vascular (? + 1 + num-cells) + [ + let r (rmin + rmax) / 2 + let theta (? * (leaf-angle + angular-spacing)) + leaf-angle / 2 + setxy (r * cos(theta)) (r * sin(theta)) + create-phloem-with vascular num-cells ;; connect to central stem + ;; Connect to a cell in your own leaf + let choice ( one-of (cells with [leaf = ?]) ) + if choice != nobody [ create-phloem-with choice ] + + become-susceptible + ] + ] + ask vasculars ;; make the vasculature stand out from the leaf cells + [ + set color green + set size 2.5 + ] +end + +;; --- helper function to pick a radius that ensures unifom distribution --- +to-report random-radius [rmin rmax] + ;; picks a radius at random such that points will be uniform in a circle + ;; pdf is r/const ; use inverse transform method + let u random-float 1 + let r sqrt(u * (rmax ^ 2 - rmin ^ 2) + rmin ^ 2 ) + report r +end + + + +to setup-leaf + ask cells + [ + ;; using random-possion to give a more realistic distribution of links per cell + let my-leaf leaf + while [ count my-links < random-poisson avg-num-plasmodesmata ] + [ + let choice (min-one-of (other cells with [(not link-neighbor? myself) and leaf = my-leaf]) + [distance myself]) + if choice != nobody [ create-plasmodesma-with choice ] + ] + ] + ;; to make the network look nicer +repeat 10 [ layout-spring turtles links 0.3 (world-width / (sqrt num-cells)) 1 ] +end + + + +;; ----- MAIN ----- + +;; This is the main process - what is activated when the user clicks "go" +to go + ;; if the user specified a duration, stop after that. + if specified-duration + [ + if ticks > num-ticks [ stop ] + ] + ;; otherwise, check if all cells are infected + if all? cells [ infected? ] + [ + ;; if they are, run 40 more times (make the graph look nice) + let i 0 + while [i <= 40] + [ + spread-virus + set i i + 1 + tick + ] + stop + ;; stop model completely + ] + ;; otherwise, continue to spread the virus + spread-virus + spread-sar + do-apoptosis-checks + record-data + tick +end + +;; ----- DATA OUTPUT ----- + +to record-data + file-open "netlogo_out.csv" + let leaf-infect-list array:to-list infect-per-leaf + foreach leaf-infect-list ;; iterate through this list + [ file-write ? ;; type number then comma + file-type ","] + file-type " ," ;; next set of columns: mod infections + let mod-leaf-infect-list array:to-list mod-infect-per-leaf + foreach mod-leaf-infect-list ;; iterate through this list + [ file-write ? ;; type number then comma + file-type ","] + file-type "\n" ;; newline + file-close ;; apparently bad things happen if you don't +end + + +;; ----- CELL PROCEDURES ----- + +;; Cell Procedures +to become-infected + ;; change global tracking variables for a first infection + if (not infected?) + [ + if (is-cell? self) [set num-infected num-infected + 1 ;; increment counters + array:set infect-per-leaf leaf (array:item infect-per-leaf leaf + 1)] + set infected? true + set resistant? false + set color red + ] + ;; regardless, pass on viral particle + set viral-count viral-count + 1 + set num-viruses num-viruses + 1 +end + +to mod-become-infected + set infected? true + set resistant? false + set color red + set mod-copy-number copy-number + 1 + set mod-num-viruses mod-num-viruses + 1 + array:set mod-infect-per-leaf leaf (array:item mod-infect-per-leaf leaf + 1) ;; increment counter +end + +to become-resistant + set resistant? true + set color blue +end + +to become-susceptible + set infected? false + set resistant? false + set color green + set copy-number 0 + set pregenomes 0 + set protein-six 0 + set viral-count 0 + set mod-copy-number 0 + set mod-pregenomes 0 + set mod-viral-count 0 +end + + +;; ---- SAR Molecule Spread & Apoptosis ---- + +;; Signalling molecules are produced (one per tick) by +;; - cells with infected neighbours +;; - resistant cells +;; Signalling molecules are spread by +;; - resistant cells -- pass on 20% their SAR each tick +;; - susceptible cells -- only pass on 10% +;; - Stems also spread SAR, but don't produce any. +;; - Infected cells do not produce or pass on SAR, but they can lyse. +;; NOTE -- don't have an integer # of molecules, since they get split. +to spread-sar + ;; initial generation of sar based on neighbouring cells being infected + ask cells + [ + if (any? link-neighbors with [infected?]) + [ set sar-level sar-level + 1 ] + let neighboured false ;; remember if a neighbour is infected + ask link-neighbors + [ + if (infected?) [ set neighboured true ] + ] + ;; if a neighbour is infected, increase this cell's sar signalling molecule + if (neighboured) [ set sar-level sar-level + 1 ] + if (resistant?) [set sar-level sar-level + 1 ] + ] + ;; assume the resistant cells are better able to spread the sar molecule + ask turtles with [resistant?] + [ + let shared-sar sar-level / 5 ;; saying half the sar-level will be spread + let num-neighbors (count link-neighbors) + ask link-neighbors + [ + set sar-level sar-level + shared-sar / num-neighbors + if (sar-level >= resistance-threshold) and (not infected?) + [ become-resistant ] + ] + set sar-level sar-level - shared-sar ;; take away what we spread + ] + ;; assume the susceptible cells can produce an okay amount of sar molecule + ask turtles with [not infected? and not resistant?] + [ + let shared-sar sar-level / 10 ;; tenth of the molecules will be shared + let num-neighbors (count link-neighbors) + ask link-neighbors + [ + set sar-level sar-level + shared-sar / num-neighbors + if (sar-level >= resistance-threshold) and (not infected?) + [ become-resistant ] + ] + set sar-level sar-level - shared-sar ;; take away what we spread + ] +end + +;; Determine whether the cell can destroy itself to help prevent viral spread +to do-apoptosis-checks + ;; if the cell is infected and can still lyse, check + ask cells with [infected?] + [ + if (sar-level >= lysis-threshold) + [ + set lysed-cells lysed-cells + 1 + die + ] + ] +end + + + +;; ----- VIRUS PROCEDURES ----- + +;; Procedure governing spread to neighbouring cells +to spread-virus + ask turtles with [infected?] + [ + if (viral-count + mod-viral-count > -1) + [ + if (random-float 100 < viral-spread-chance) + [ + set viral-count viral-count - 1 ;; take away the one that we will spread + if any? link-neighbors with [not resistant?] ;; make sure there's a valid target + [ + ask one-of link-neighbors with [not resistant?] ;; put it into that target + [ become-infected] + ] + ] + ] + ] +end + + +to assemble-virus + ;; viral-count increases with P6 and pregenomes + ;; p6 increases with copy number + ;; pregenomes increases with copy number + ;; copy number increases with viral count + ;; -- viral count should be the thing we spread + ask cells with [infected?] + [ + ;; 35S RNA formation + if (viral-count + mod-viral-count < 500) + [ + set pregenomes pregenomes + 0.01 * copy-number + ;set mod-viral-count mod-viral-count + mod-copy-number + ] + ;; P6 production + if (protein-six < 1000) + [ + set protein-six protein-six + 0.01 * copy-number + ] + ;; Viral assembly + if (viral-count + mod-viral-count < 500) + [ + set viral-count viral-count + 0.01 * protein-six * pregenomes + ;set mod-viral-count mod-viral-count + mod-copy-number + ] + ;; Reentry in nucleus + if (copy-number + mod-copy-number < 100) + [ + set copy-number copy-number + 0.01 * viral-count + ;set mod-copy-number 1.05 * mod-copy-number + ] + ] +end +@#$#@#$#@ +GRAPHICS-WINDOW +691 +12 +1279 +621 +22 +22 +12.85 +1 +10 +1 +1 +1 +0 +0 +0 +1 +-22 +22 +-22 +22 +0 +0 +1 +ticks +30.0 + +BUTTON +116 +288 +179 +321 +go +go +T +1 +T +OBSERVER +NIL +NIL +NIL +NIL +1 + +SLIDER +22 +102 +196 +135 +initial-infection-sites +initial-infection-sites +1 +4 +4 +1 +1 +NIL +HORIZONTAL + +SLIDER +20 +10 +192 +43 +num-cells +num-cells +200 +600 +540 +10 +1 +NIL +HORIZONTAL + +SLIDER +20 +49 +208 +82 +avg-num-plasmodesmata +avg-num-plasmodesmata +1 +10 +8 +1 +1 +NIL +HORIZONTAL + +PLOT +231 +475 +454 +672 +#infected over time +ticks +#infected cells +0.0 +50.0 +0.0 +50.0 +true +false +"set-plot-x-range 0 num-ticks\nset-plot-y-range 0 num-cells" "" +PENS +"infected" 1.0 0 -13791810 true "" "plot num-infected" + +BUTTON +38 +289 +101 +322 +setup +setup +NIL +1 +T +OBSERVER +NIL +NIL +NIL +NIL +1 + +SLIDER +25 +356 +197 +389 +viral-spread-chance +viral-spread-chance +1 +20 +12 +0.5 +1 +NIL +HORIZONTAL + +SLIDER +21 +227 +193 +260 +num-ticks +num-ticks +0 +500 +459 +1 +1 +NIL +HORIZONTAL + +SWITCH +22 +190 +177 +223 +specified-duration +specified-duration +0 +1 +-1000 + +PLOT +466 +485 +666 +635 +Number of Viruses +ticks +#viruses +0.0 +10.0 +1.0 +1000.0 +true +false +"set-plot-x-range 0 num-ticks\nset-plot-y-range 0 num-cells" "" +PENS +"default" 1.0 0 -16777216 true "" "plot (num-viruses + mod-num-viruses)" + +SLIDER +22 +141 +215 +174 +founder-population-viruses +founder-population-viruses +400 +600 +460 +10 +1 +NIL +HORIZONTAL + +SLIDER +24 +446 +196 +479 +lysis-threshold +lysis-threshold +1 +10000 +2676 +1 +1 +NIL +HORIZONTAL + +PLOT +19 +490 +219 +640 +Lysed Cells +ticks +#cells +0.0 +10.0 +0.0 +10.0 +true +false +"set-plot-x-range 0 num-ticks\nset-plot-y-range 0 10" "" +PENS +"default" 1.0 0 -16777216 true "" "plot lysed-cells" + +SLIDER +23 +410 +195 +443 +resistance-threshold +resistance-threshold +1 +100 +34 +1 +1 +NIL +HORIZONTAL + +SLIDER +24 +327 +196 +360 +num-leaves +num-leaves +1 +10 +7 +1 +1 +NIL +HORIZONTAL + +@#$#@#$#@ +## WHAT IS IT? + +This is a model tracking viral spread in a plant-structure made of leaf cells and vascular cells. The spatial locations of the cells are divided into "leaves", and individual cells are connected by plasmodesmata. + + +## HOW IT WORKS + +The model begins by creating all of the cells - it places them in space (in 4 leaves separated by the coodrinate axes) and iteratively goes through the cells, giving each a random number of connections. + +All the cells start as susceptible, except for some small initial infection. Then the virus spreads along the plasmodesmata connections as time progresses. + +In this model there's also a chance of cells becoming resistant. This is triggered by either proximity to infected cells, or by spreading among + + +## HOW TO USE IT + +Set the sliders as you see fit and click setup. Hit go to see what happens! + + +## THINGS TO NOTICE + +How does the viral infection curve change as # of connections is increased and viral spread chance is decreased? + + +## THINGS TO TRY + +Move the sliders! And note the variations in the random setup, especially as it concerns connections between different leaves. + + +## EXTENDING THE MODEL + +Giving appropriate parameters for the viral spread chance. + + +## NETLOGO FEATURES + +(interesting or unusual features of NetLogo that the model uses, particularly in the Code tab; or where workarounds were needed for missing features) + + +## RELATED MODELS + +(models in the NetLogo Models Library and elsewhere which are of related interest) + + +## CREDITS AND REFERENCES + +UWaterloo's 2015 iGEM team +Zoë Humphries & Robert Gooding-Townsend +@#$#@#$#@ +default +true +0 +Polygon -7500403 true true 150 5 40 250 150 205 260 250 + +airplane +true +0 +Polygon -7500403 true true 150 0 135 15 120 60 120 105 15 165 15 195 120 180 135 240 105 270 120 285 150 270 180 285 210 270 165 240 180 180 285 195 285 165 180 105 180 60 165 15 + +arrow +true +0 +Polygon -7500403 true true 150 0 0 150 105 150 105 293 195 293 195 150 300 150 + +box +false +0 +Polygon -7500403 true true 150 285 285 225 285 75 150 135 +Polygon -7500403 true true 150 135 15 75 150 15 285 75 +Polygon -7500403 true true 15 75 15 225 150 285 150 135 +Line -16777216 false 150 285 150 135 +Line -16777216 false 150 135 15 75 +Line -16777216 false 150 135 285 75 + +bug +true +0 +Circle -7500403 true true 96 182 108 +Circle -7500403 true true 110 127 80 +Circle -7500403 true true 110 75 80 +Line -7500403 true 150 100 80 30 +Line -7500403 true 150 100 220 30 + +butterfly +true +0 +Polygon -7500403 true true 150 165 209 199 225 225 225 255 195 270 165 255 150 240 +Polygon -7500403 true true 150 165 89 198 75 225 75 255 105 270 135 255 150 240 +Polygon -7500403 true true 139 148 100 105 55 90 25 90 10 105 10 135 25 180 40 195 85 194 139 163 +Polygon -7500403 true true 162 150 200 105 245 90 275 90 290 105 290 135 275 180 260 195 215 195 162 165 +Polygon -16777216 true false 150 255 135 225 120 150 135 120 150 105 165 120 180 150 165 225 +Circle -16777216 true false 135 90 30 +Line -16777216 false 150 105 195 60 +Line -16777216 false 150 105 105 60 + +car +false +0 +Polygon -7500403 true true 300 180 279 164 261 144 240 135 226 132 213 106 203 84 185 63 159 50 135 50 75 60 0 150 0 165 0 225 300 225 300 180 +Circle -16777216 true false 180 180 90 +Circle -16777216 true false 30 180 90 +Polygon -16777216 true false 162 80 132 78 134 135 209 135 194 105 189 96 180 89 +Circle -7500403 true true 47 195 58 +Circle -7500403 true true 195 195 58 + +circle +false +0 +Circle -7500403 true true 0 0 300 + +circle 2 +false +0 +Circle -7500403 true true 0 0 300 +Circle -16777216 true false 30 30 240 + +cow +false +0 +Polygon -7500403 true true 200 193 197 249 179 249 177 196 166 187 140 189 93 191 78 179 72 211 49 209 48 181 37 149 25 120 25 89 45 72 103 84 179 75 198 76 252 64 272 81 293 103 285 121 255 121 242 118 224 167 +Polygon -7500403 true true 73 210 86 251 62 249 48 208 +Polygon -7500403 true true 25 114 16 195 9 204 23 213 25 200 39 123 + +cylinder +false +0 +Circle -7500403 true true 0 0 300 + +dot +false +0 +Circle -7500403 true true 90 90 120 + +face happy +false +0 +Circle -7500403 true true 8 8 285 +Circle -16777216 true false 60 75 60 +Circle -16777216 true false 180 75 60 +Polygon -16777216 true false 150 255 90 239 62 213 47 191 67 179 90 203 109 218 150 225 192 218 210 203 227 181 251 194 236 217 212 240 + +face neutral +false +0 +Circle -7500403 true true 8 7 285 +Circle -16777216 true false 60 75 60 +Circle -16777216 true false 180 75 60 +Rectangle -16777216 true false 60 195 240 225 + +face sad +false +0 +Circle -7500403 true true 8 8 285 +Circle -16777216 true false 60 75 60 +Circle -16777216 true false 180 75 60 +Polygon -16777216 true false 150 168 90 184 62 210 47 232 67 244 90 220 109 205 150 198 192 205 210 220 227 242 251 229 236 206 212 183 + +fish +false +0 +Polygon -1 true false 44 131 21 87 15 86 0 120 15 150 0 180 13 214 20 212 45 166 +Polygon -1 true false 135 195 119 235 95 218 76 210 46 204 60 165 +Polygon -1 true false 75 45 83 77 71 103 86 114 166 78 135 60 +Polygon -7500403 true true 30 136 151 77 226 81 280 119 292 146 292 160 287 170 270 195 195 210 151 212 30 166 +Circle -16777216 true false 215 106 30 + +flag +false +0 +Rectangle -7500403 true true 60 15 75 300 +Polygon -7500403 true true 90 150 270 90 90 30 +Line -7500403 true 75 135 90 135 +Line -7500403 true 75 45 90 45 + +flower +false +0 +Polygon -10899396 true false 135 120 165 165 180 210 180 240 150 300 165 300 195 240 195 195 165 135 +Circle -7500403 true true 85 132 38 +Circle -7500403 true true 130 147 38 +Circle -7500403 true true 192 85 38 +Circle -7500403 true true 85 40 38 +Circle -7500403 true true 177 40 38 +Circle -7500403 true true 177 132 38 +Circle -7500403 true true 70 85 38 +Circle -7500403 true true 130 25 38 +Circle -7500403 true true 96 51 108 +Circle -16777216 true false 113 68 74 +Polygon -10899396 true false 189 233 219 188 249 173 279 188 234 218 +Polygon -10899396 true false 180 255 150 210 105 210 75 240 135 240 + +house +false +0 +Rectangle -7500403 true true 45 120 255 285 +Rectangle -16777216 true false 120 210 180 285 +Polygon -7500403 true true 15 120 150 15 285 120 +Line -16777216 false 30 120 270 120 + +leaf +false +0 +Polygon -7500403 true true 150 210 135 195 120 210 60 210 30 195 60 180 60 165 15 135 30 120 15 105 40 104 45 90 60 90 90 105 105 120 120 120 105 60 120 60 135 30 150 15 165 30 180 60 195 60 180 120 195 120 210 105 240 90 255 90 263 104 285 105 270 120 285 135 240 165 240 180 270 195 240 210 180 210 165 195 +Polygon -7500403 true true 135 195 135 240 120 255 105 255 105 285 135 285 165 240 165 195 + +line +true +0 +Line -7500403 true 150 0 150 300 + +line half +true +0 +Line -7500403 true 150 0 150 150 + +pentagon +false +0 +Polygon -7500403 true true 150 15 15 120 60 285 240 285 285 120 + +person +false +0 +Circle -7500403 true true 110 5 80 +Polygon -7500403 true true 105 90 120 195 90 285 105 300 135 300 150 225 165 300 195 300 210 285 180 195 195 90 +Rectangle -7500403 true true 127 79 172 94 +Polygon -7500403 true true 195 90 240 150 225 180 165 105 +Polygon -7500403 true true 105 90 60 150 75 180 135 105 + +plant +false +0 +Rectangle -7500403 true true 135 90 165 300 +Polygon -7500403 true true 135 255 90 210 45 195 75 255 135 285 +Polygon -7500403 true true 165 255 210 210 255 195 225 255 165 285 +Polygon -7500403 true true 135 180 90 135 45 120 75 180 135 210 +Polygon -7500403 true true 165 180 165 210 225 180 255 120 210 135 +Polygon -7500403 true true 135 105 90 60 45 45 75 105 135 135 +Polygon -7500403 true true 165 105 165 135 225 105 255 45 210 60 +Polygon -7500403 true true 135 90 120 45 150 15 180 45 165 90 + +sheep +false +15 +Circle -1 true true 203 65 88 +Circle -1 true true 70 65 162 +Circle -1 true true 150 105 120 +Polygon -7500403 true false 218 120 240 165 255 165 278 120 +Circle -7500403 true false 214 72 67 +Rectangle -1 true true 164 223 179 298 +Polygon -1 true true 45 285 30 285 30 240 15 195 45 210 +Circle -1 true true 3 83 150 +Rectangle -1 true true 65 221 80 296 +Polygon -1 true true 195 285 210 285 210 240 240 210 195 210 +Polygon -7500403 true false 276 85 285 105 302 99 294 83 +Polygon -7500403 true false 219 85 210 105 193 99 201 83 + +square +false +0 +Rectangle -7500403 true true 30 30 270 270 + +square 2 +false +0 +Rectangle -7500403 true true 30 30 270 270 +Rectangle -16777216 true false 60 60 240 240 + +star +false +0 +Polygon -7500403 true true 151 1 185 108 298 108 207 175 242 282 151 216 59 282 94 175 3 108 116 108 + +target +false +0 +Circle -7500403 true true 0 0 300 +Circle -16777216 true false 30 30 240 +Circle -7500403 true true 60 60 180 +Circle -16777216 true false 90 90 120 +Circle -7500403 true true 120 120 60 + +tree +false +0 +Circle -7500403 true true 118 3 94 +Rectangle -6459832 true false 120 195 180 300 +Circle -7500403 true true 65 21 108 +Circle -7500403 true true 116 41 127 +Circle -7500403 true true 45 90 120 +Circle -7500403 true true 104 74 152 + +triangle +false +0 +Polygon -7500403 true true 150 30 15 255 285 255 + +triangle 2 +false +0 +Polygon -7500403 true true 150 30 15 255 285 255 +Polygon -16777216 true false 151 99 225 223 75 224 + +truck +false +0 +Rectangle -7500403 true true 4 45 195 187 +Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194 +Rectangle -1 true false 195 60 195 105 +Polygon -16777216 true false 238 112 252 141 219 141 218 112 +Circle -16777216 true false 234 174 42 +Rectangle -7500403 true true 181 185 214 194 +Circle -16777216 true false 144 174 42 +Circle -16777216 true false 24 174 42 +Circle -7500403 false true 24 174 42 +Circle -7500403 false true 144 174 42 +Circle -7500403 false true 234 174 42 + +turtle +true +0 +Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210 +Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105 +Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105 +Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87 +Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210 +Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99 + +wheel +false +0 +Circle -7500403 true true 3 3 294 +Circle -16777216 true false 30 30 240 +Line -7500403 true 150 285 150 15 +Line -7500403 true 15 150 285 150 +Circle -7500403 true true 120 120 60 +Line -7500403 true 216 40 79 269 +Line -7500403 true 40 84 269 221 +Line -7500403 true 40 216 269 79 +Line -7500403 true 84 40 221 269 + +wolf +false +0 +Polygon -16777216 true false 253 133 245 131 245 133 +Polygon -7500403 true true 2 194 13 197 30 191 38 193 38 205 20 226 20 257 27 265 38 266 40 260 31 253 31 230 60 206 68 198 75 209 66 228 65 243 82 261 84 268 100 267 103 261 77 239 79 231 100 207 98 196 119 201 143 202 160 195 166 210 172 213 173 238 167 251 160 248 154 265 169 264 178 247 186 240 198 260 200 271 217 271 219 262 207 258 195 230 192 198 210 184 227 164 242 144 259 145 284 151 277 141 293 140 299 134 297 127 273 119 270 105 +Polygon -7500403 true true -1 195 14 180 36 166 40 153 53 140 82 131 134 133 159 126 188 115 227 108 236 102 238 98 268 86 269 92 281 87 269 103 269 113 + +x +false +0 +Polygon -7500403 true true 270 75 225 30 30 225 75 270 +Polygon -7500403 true true 30 75 75 30 270 225 225 270 + +@#$#@#$#@ +NetLogo 5.2.0 +@#$#@#$#@ +@#$#@#$#@ +@#$#@#$#@ +@#$#@#$#@ +@#$#@#$#@ +default +0.0 +-0.2 0 0.0 1.0 +0.0 1 1.0 0.0 +0.2 0 0.0 1.0 +link direction +true +0 +Line -7500403 true 150 150 90 180 +Line -7500403 true 150 150 210 180 + +@#$#@#$#@ +0 +@#$#@#$#@